Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Methionyl-tRNA formyltransferase, mitochondrial.

Parent gene

Gene structure

  • The exon-intron structure of all isoforms are indicated below. CDS regions are colored in green. TSS and TTs that were predicted with CTR-Seq data are indicated in solid circle and squares, respectively. More specific data are shown in the table below.

Chromosome Gene Transcript Category ID Start End
chr_3 g2508 g2508.t2 TSS g2508.t2 18333862 18333862
chr_3 g2508 g2508.t2 isoform g2508.t2 18334439 18335460
chr_3 g2508 g2508.t2 exon g2508.t2.exon1 18334439 18334560
chr_3 g2508 g2508.t2 cds g2508.t2.CDS1 18334439 18334560
chr_3 g2508 g2508.t2 exon g2508.t2.exon2 18334616 18335460
chr_3 g2508 g2508.t2 cds g2508.t2.CDS2 18334616 18335459
chr_3 g2508 g2508.t2 TTS g2508.t2 18335491 18335491

Sequences

>g2508.t2 Gene=g2508 Length=967
ATGATTTTTAGGAATTTTTGTCATAAAATAAAATGGAAATATTTAGAATTATCTCGTAAT
TATTCACATAAAATTTTATTTTTCGGAACAGATAATTTCTCACTTCCATCATTAAAATTA
ATAACTAAACAAAATGATCTATATTCACGTCTTGAGGTTGTCACTTCTTTTAAATCAAAG
AAAAATCCAATAAAAGACTTTGCTAACGAACAAAAATTACCTGTGCATGATTGGGAAAGT
CTTAAAAACGATTTAAAAATATTTAGTGAATTTGACATAGGTTTAGTTGTTTCTTTTGGT
CATTTAATTCCTGAAAATATTATTAATAATTTTCATAAAGGGATGCTAAATGTACATGCA
AGTCTACTGCCAAAATATCGAGGTGCGAGTCCTATAATTTACGCTATAAAAAATCATGAA
ACTATAACAGGTGTATCAATAATGAAAATCAAGGCAAAAAAGTTTGATGTAGGGGATGTA
CTTGCGATGAAAGAAGTATCTATAACAGATGACATTCTTATGTCAGAATTACACGACCAA
TTAGCTAATTTAGGAGCACAATTATTAATCGATTGTCTCAAACATTTAGAAGAATGTAAG
CCAATAAAGCAAGACGAGAGCCAAGCATCATACGCACCTAAAATTGATAAAGAATTTTGC
AAAGTAAGATGGAATGAAATGAGTGCACGTGAGATTTATGATTTATACAGAGCACTCTAT
TCTTACAAGCATGTGTTGACAACATTTAAAAATGAACCGGTTAAGTTGTTAGAATTAAAA
AAATCTAATGAAGTCATTGAATATAACATTGCTGGACATTTAAAATTTTGTAAAAAAACG
AAAAAACTATTAGTGCATTGTGTTGATGGTGAATGTATAGAAATTAATAAATTACTGATA
GCTAAAAAAGTGATGAGTGCATCAGATTTTAATAATGGATTCTTAAAAAACATAAATGAT
TTTGAAA

>g2508.t2 Gene=g2508 Length=322
MIFRNFCHKIKWKYLELSRNYSHKILFFGTDNFSLPSLKLITKQNDLYSRLEVVTSFKSK
KNPIKDFANEQKLPVHDWESLKNDLKIFSEFDIGLVVSFGHLIPENIINNFHKGMLNVHA
SLLPKYRGASPIIYAIKNHETITGVSIMKIKAKKFDVGDVLAMKEVSITDDILMSELHDQ
LANLGAQLLIDCLKHLEECKPIKQDESQASYAPKIDKEFCKVRWNEMSAREIYDLYRALY
SYKHVLTTFKNEPVKLLELKKSNEVIEYNIAGHLKFCKKTKKLLVHCVDGECIEINKLLI
AKKVMSASDFNNGFLKNINDFE

Protein features from InterProScan

Transcript Database ID Name Start End E.value
11 g2508.t2 CDD cd08646 FMT_core_Met-tRNA-FMT_N 24 215 0
10 g2508.t2 CDD cd08704 Met_tRNA_FMT_C 218 307 0
7 g2508.t2 Gene3D G3DSA:3.40.50.170 Formyltransferase 18 216 0
8 g2508.t2 Gene3D G3DSA:3.10.25.10 - 217 321 0
3 g2508.t2 PANTHER PTHR11138 METHIONYL-TRNA FORMYLTRANSFERASE 18 318 0
4 g2508.t2 PANTHER PTHR11138:SF0 METHIONYL-TRNA FORMYLTRANSFERASE, MITOCHONDRIAL 18 318 0
1 g2508.t2 Pfam PF00551 Formyl transferase 58 191 0
2 g2508.t2 Pfam PF02911 Formyl transferase, C-terminal domain 214 314 0
5 g2508.t2 SUPERFAMILY SSF53328 Formyltransferase 24 217 0
6 g2508.t2 SUPERFAMILY SSF50486 FMT C-terminal domain-like 215 314 0
9 g2508.t2 TIGRFAM TIGR00460 fmt: methionyl-tRNA formyltransferase 24 319 0

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

GO terms from InterProScan

GOID TERM ONTOLOGY
GO:0071951 conversion of methionyl-tRNA to N-formyl-methionyl-tRNA BP
GO:0009058 biosynthetic process BP
GO:0016742 hydroxymethyl-, formyl- and related transferase activity MF
GO:0003824 catalytic activity MF
GO:0004479 methionyl-tRNA formyltransferase activity MF

KEGG

Orthology

Pathway

  • This transcript belongs to the following pathways

Expression

Transcript expression in Pv11 cells

TPM values are indicated as average +/- STDEV.

Differential expression

Differentially expressed genes were identified with DESeq2 using the ‘run_DE_analysis.pl’ script from Trinity. Transcripts were determined as differentially expressed when (1) FDR < 0.05 (2) fold change > 2 (TPM calculated by RSEM). DE information and fold change between conditions are indicated in the plot below.

Raw TPM values